192
Views
10
CrossRef citations to date
0
Altmetric
Article

Deciphering the transcription factor-microRNA-target gene regulatory network associated with graphene oxide cytotoxicity

, , , , &
Pages 1014-1026 | Received 15 Nov 2017, Accepted 15 Aug 2018, Published online: 16 Oct 2018

References

  • Bajpai, R., and G. P. Nagaraju. 2017. “Specificity Protein 1: Its Role in Colorectal Cancer Progression and Metastasis.” Critical Reviews in Oncology/Hematology 113: 1–7. doi:10.1016/j.critrevonc.2017.02.024
  • Barrett, T., S. E. Wilhite, P. Ledoux, C. Evangelista, I. F. Kim, M. Tomashevsky, K. A. Marshall, et al. 2012. “NCBI GEO: archive for Functional Genomics Data Sets—Update.” Nucleic Acids Research 41 (D1): D991–5. doi:10.1093/nar/gks1193
  • Bartel, D. P. 2004. “MicroRNAs: Genomics, Biogenesis, Mechanism, and Function.” cell 116 (2): 281–97. doi:10.1016/S0092-8674(04)00045-5
  • Butz, H., K. Rácz, L. Hunyady, and A. Patócs. 2012. “Crosstalk between TGF-β Signaling and the microRNA Machinery.” Trends in Pharmacological Sciences 33 (7): 382–93. doi:10.1016/j.tips.2012.04.003
  • Carvalho, B. S., and R. A. Irizarry. 2010. “A Framework for Oligonucleotide Microarray Preprocessing.” Bioinformatics 26 (19): 2363–7. doi:10.1093/bioinformatics/btq431
  • Chatterjee, N., H.-J. Eom, and J. Choi. 2014. “A Systems Toxicology Approach to the Surface Functionality Control of Graphene–Cell Interactions.” Biomaterials 35 (4): 1109–27. doi:10.1016/j.biomaterials.2013.09.108
  • Chekmenev, D., C. Haid, and A. Kel. 2005. “P-Match: transcription Factor Binding Site Search by Combining Patterns and Weight Matrices.” Nucleic Acids Research 33 (Web Server): W432–7. doi:10.1093/nar/gki441
  • Chen, C.-Y., S.-T. Chen, C.-S. Fuh, H.-F. Juan, and H.-C. Huang. 2011. “Coregulation of Transcription Factors and microRNAs in Human Transcriptional Regulatory Network.” BMC Bioinformatics 12 (Suppl 1): S41. doi:10.1186/1471-2105-12-S1-S41
  • Chen, K., and N. Rajewsky. 2007. “The Evolution of Gene Regulation by Transcription Factors and microRNAs.” Nature Reviews. Genetics 8 (2): 93. doi:10.1038/nrg1990
  • Chien, C.-H., Y.-M. Sun, W.-C. Chang, P.-Y. Chiang-Hsieh, T.-Y. Lee, W.-C. Tsai, J.-T. Horng, A.-P. Tsou, and H.-D. Huang. 2011. “Identifying Transcriptional Start Sites of Human microRNAs Based on High-Throughput Sequencing Data.” Nucleic Acids Research 39 (21): 9345–56. doi:10.1093/nar/gkr604
  • Chou, C.-H., N.-W. Chang, S. Shrestha, S.-D. Hsu, Y.-L. Lin, W.-H. Lee, C.-D. Yang, et al. 2016. “miRTarBase 2016: updates to the Experimentally Validated miRNA-Target Interactions Database.” Nucleic Acids Research 44 (D1): D239–D247. doi:10.1093/nar/gkv1258
  • Cooper, S. J., N. D. Trinklein, E. D. Anton, L. Nguyen, and R. M. Myers. 2005. “Comprehensive Analysis of Transcriptional Promoter Structure and Function in 1% of the Human Genome.” Genome Research 16 (1): 1–10. doi:10.1101/gr.4222606
  • Davis, A. P., C. J. Grondin, R. J. Johnson, D. Sciaky, B. L. King, R. Mcmorran, J. Wiegers, T. C. Wiegers, and C. J. Mattingly. 2017. “The Comparative Toxicogenomics Database: update 2017.” Nucleic Acids Research 45 (D1): D972–D978. doi:10.1093/nar/gkw838
  • Fahmy, M.,. H. Jazayeri, M. Razavi, M. Hashemi, M. Omidi, M. Farahani, E. Salahinejad, A. Yadegari, S. Pitcher, and L. Tayebi. 2016. “Biomedical Applications of Intelligent Nanomaterials.” Intelligent Nanomaterials 199: 245.
  • Feng, L., S. Zhang, and Z. Liu. 2011. “Graphene Based Gene transfection.” Nanoscale 3 (3): 1252–7. doi:10.1039/c0nr00680g
  • Gautier, L., L. Cope, B. M. Bolstad, and R. A. Irizarry. 2004. “ affy-analysis of Affymetrix GeneChip data at the probe level.” Bioinformatics (Oxford, England) 20 (3): 307–315. doi:10.1093/bioinformatics/btg405
  • Goenka, S., V. Sant, and S. Sant. 2014. “Graphene-Based Nanomaterials for Drug Delivery and Tissue Engineering.” Journal of Controlled Release: Official Journal of the Controlled Release Society 173: 75–88. doi:10.1016/j.jconrel.2013.10.017
  • Halappanavar, S., P. Jackson, A. Williams, K. A. Jensen, K. S. Hougaard, U. Vogel, C. L. Yauk, and H. Wallin. 2011. “Pulmonary Response to Surface‐Coated Nanotitanium Dioxide Particles Includes Induction of Acute Phase Response Genes, Inflammatory Cascades, and Changes in microRNAs: A Toxicogenomic Study.” Environmental and Molecular Mutagenesis 52 (6): 425–439. doi:10.1002/em.20639
  • Han, H., J.-W. Cho, S. Lee, A. Yun, H. Kim, D. Bae, S. Yang, et al. 2018. “TRRUST v2: An Expanded Reference Database of Human and Mouse Transcriptional Regulatory Interactions.” Nucleic Acids Research 46 (D1): D380–D386. doi:10.1093/nar/gkx1013
  • Hobert, O. 2008. “Gene Regulation by Transcription Factors and microRNAs.” Science (New York, N.Y.) 319 (5871): 1785–1786. doi:10.1126/science.1151651
  • Huang, D. W., B. T. Sherman, Q. Tan, J. R. Collins, W. G. Alvord, J. Roayaei, R. Stephens, M. W. Baseler, H. C. Lane, and R. A. Lempicki. 2007. “The DAVID Gene Functional Classification Tool: A Novel Biological Module-Centric Algorithm to Functionally Analyze Large Gene Lists.” Genome Biology 8 (9): R183. doi:10.1186/gb-2007-8-9-r183
  • Huang, Y., X. Lü, and J. Ma. 2014. “Toxicity of Silver Nanoparticles to Human Dermal Fibroblasts on microRNA Level.” Journal of Biomedical Nanotechnology 10 (11): 3304–3317. doi:10.1166/jbn.2014.1974
  • Huang, Y., X. Lü, Y. Qu, Y. Yang, and S. Wu. 2015. “MicroRNA Sequencing and Molecular Mechanisms Analysis of the Effects of Gold Nanoparticles on Human Dermal Fibroblasts.” Biomaterials 37: 13–24. doi:10.1016/j.biomaterials.2014.10.042
  • Kang, Y., J. Liu, J. Wu, Q. Yin, H. Liang, A. Chen, and L. Shao. 2017. “Graphene Oxide and Reduced Graphene Oxide Induced Neural Pheochromocytoma-Derived PC12 Cell Lines Apoptosis and Cell Cycle Alterations via the ERK Signaling Pathways.” International Journal of Nanomedicine 12: 5501. doi:10.2147/IJN.S141032
  • Killcoyne, S., G. W. Carter, J. Smith, and J. Boyle. 2009. “Cytoscape: A Community-Based Framework for Network Modeling.” Protein Networks and Pathway Analysis 219: 239.
  • Kim, H., R. Namgung, K. Singha, I.-K. Oh, and W. J. Kim. 2011. “Graphene Oxide–Polyethylenimine Nanoconstruct as a Gene Delivery Vector and Bioimaging Tool.” Bioconjugate Chemistry 22 (12): 2558–2567. doi:10.1021/bc200397j
  • LA, W. G., S. Park, H. H. Yoon, G. J. Jeong, T. J. Lee, S. H. Bhang, J. Y. Han, K. Char, and B. S. Kim. 2013. “Delivery of a Therapeutic Protein for Bone Regeneration from a Substrate Coated with Graphene Oxide.” Small (Weinheim an Der Bergstrasse, Germany) 9 (23): 4051–4060. doi:10.1002/smll.201300571
  • Li, Y., Y. Liu, Y. Fu, T. Wei, L. Le Guyader, G. Gao, R.-S. Liu, Y.-Z. Chang, and C. Chen. 2012. “The Triggering of Apoptosis in Macrophages by Pristine Graphene through the MAPK and TGF-Beta Signaling Pathways.” Biomaterials 33 (2): 402–411. doi:10.1016/j.biomaterials.2011.09.091
  • Li, Y., Q. Wu, Y. Zhao, Y. Bai, P. Chen, T. Xia, and D. Wang. 2014. “Response of microRNAs to in Vitro Treatment with Graphene Oxide.” ACS Nano 8 (3): 2100–2110. doi:10.1021/nn4065378
  • Liang, S., S. Xu, D. Zhang, J. He, and M. Chu. 2015. “Reproductive Toxicity of Nanoscale Graphene Oxide in Male Mice.” Nanotoxicology 9 (1): 92–105. doi:10.3109/17435390.2014.893380
  • Lin, J., X. Chen, and P. Huang. 2016. “Graphene-Based Nanomaterials for Bioimaging.” Advanced Drug Delivery Reviews 105 (Pt B): 242–254. doi:10.1016/j.addr.2016.05.013
  • Liu, J., L. Cui, and D. Losic. 2013. “Graphene and Graphene Oxide as New Nanocarriers for Drug Delivery Applications.” Acta Biomaterialia 9 (12): 9243–9257. doi:10.1016/j.actbio.2013.08.016
  • Liu, M., F. Bi, X. Zhou, and Y. Zheng. 2012. “Rho GTPase Regulation by miRNAs and Covalent Modifications.” Trends in Cell Biology 22 (7): 365–373. doi:10.1016/j.tcb.2012.04.004
  • Liu, Y., Y. Luo, J. Wu, Y. Wang, X. Yang, R. Yang, B. Wang, J. Yang, and N. Zhang. 2013. “Graphene Oxide Can Induce in Vitro and in Vivo Mutagenesis.” Scientific Reports 3: 3469. doi:10.1038/srep03469
  • Liu, Z., J. T. Robinson, X. Sun, and H. Dai. 2008. “PEGylated Nanographene Oxide for Delivery of Water-Insoluble Cancer Drugs.” Journal of the American Chemical Society 130 (33): 10876–10877. doi:10.1021/ja803688x
  • Lu, C.-J., X.-F. Jiang, M. Junaid, Y.-B. Ma, P.-P. Jia, H.-B. Wang, and D.-S. Pei. 2017. “Graphene Oxide Nanosheets Induce DNA Damage and Activate the Base Excision Repair (BER) Signaling Pathway Both In Vitro and In Vivo.” Chemosphere 184, 795–805. doi:10.1016/j.chemosphere.2017.06.049
  • Lu, M., Q. Zhang, M. Deng, J. Miao, Y. Guo, W. Gao, and Q. Cui. 2008. “An Analysis of Human microRNA and Disease associations.” PloS One 3 (10): e3420. doi:10.1371/journal.pone.0003420
  • Martinez, N. J., and A. J. Walhout. 2009. “The Interplay between Transcription Factors and microRNAs in Genome‐Scale Regulatory Networks.” Bioessays 31 (4): 435–445. doi:10.1002/bies.200800212
  • Milo, R., S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon. 2002. “Network Motifs: simple Building Blocks of Complex networks.” Science (New York, N.Y.) 298 (5594): 824–827. doi:10.1126/science.298.5594.824
  • Nurunnabi, M., K. Parvez, M. Nafiujjaman, V. Revuri, H. A. Khan, X. Feng, and Y.-K. Lee. 2015. “Bioapplication of Graphene Oxide Derivatives: drug/Gene Delivery, Imaging, Polymeric Modification, Toxicology, Therapeutics and Challenges.” RSC Advances 5 (52): 42141–42161. doi:10.1039/C5RA04756K
  • Oh, J.-H., M.-Y. Son, M.-S. Choi, S. Kim, A.-Y. Choi, H.-A. Lee, K.-S. Kim, J. Kim, C. W. Song, and S. Yoon. 2016. “Integrative Analysis of Genes and miRNA Alterations in Human Embryonic Stem Cells-Derived Neural Cells after Exposure to Silver Nanoparticles.” Toxicology and Applied Pharmacology 299: 8–23. doi:10.1016/j.taap.2015.11.004
  • Orecchioni, M., D. Bedognetti, L. Newman, C. Fuoco, F. Spada, W. Hendrickx, F. M. Marincola, et al. 2017. “Single-Cell Mass Cytometry and Transcriptome Profiling Reveal the Impact of Graphene on Human Immune Cells.” Nature Communications 8 (1): 1109. doi:10.1038/s41467-017-01015-3
  • Pigazzi, M., E. Manara, E. Baron, and G. Basso. 2009. “miR-34b Targets Cyclic AMP–Responsive Element Binding Protein in Acute Myeloid Leukemia.” Cancer Research 69 (6): 2471–2478. doi:10.1158/0008-5472.CAN-08-3404
  • Sakamoto, K. M., and D. A. Frank. 2009. “CREB in the Pathophysiology of Cancer: implications for Targeting Transcription Factors for Cancer Therapy.” Clinical Cancer Research 15 (8): 2583–2587. doi:10.1158/1078-0432.CCR-08-1137
  • Seabra, A. B., A. J. Paula, R. de Lima, O. L. Alves, and N. Durán. 2014. “Nanotoxicity of Graphene and Graphene Oxide.” Chemical Research in Toxicology 27 (2): 159–168. doi:10.1021/tx400385x
  • Shao, Y., J. Wang, H. Wu, J. Liu, I. A. Aksay, and Y. Lin. 2010. “Graphene Based Electrochemical Sensors and Biosensors: A Review.” Electroanalysis 22 (10): 1027–1036. doi:10.1002/elan.200900571
  • Snyder-Talkington, B. N., C. Dong, L. M. Sargent, D. W. Porter, L. M. Staska, A. F. Hubbs, R. Raese, et al. 2016. “mRNAs and miRNAs in Whole Blood Associated with Lung Hyperplasia, Fibrosis, and Bronchiolo‐Alveolar Adenoma and Adenocarcinoma after Multi‐Walled Carbon Nanotube Inhalation Exposure in Mice.” Journal of Applied Toxicology 36 (1): 161–174. doi:10.1002/jat.3157
  • Sollome, J., E. Martin, P. Sethupathy, and R. C. Fry. 2016. “Environmental Contaminants and microRNA Regulation: transcription Factors as Regulators of Toxicant-Altered microRNA Expression.” Toxicology and Applied Pharmacology 312: 61–66. doi:10.1016/j.taap.2016.06.009
  • Steven, A., and B. Seliger. 2016. “Control of CREB Expression in Tumors: From Molecular Mechanisms and Signal Transduction Pathways to Therapeutic Target.” Oncotarget 7 (23): 35454.
  • Szklarczyk, D., A. Santos, C. VON Mering, L. J. Jensen, P. Bork, and M. Kuhn. 2016. “STITCH 5: augmenting Protein–Chemical Interaction Networks with Tissue and Affinity Data.” Nucleic Acids Research 44 (D1): D380–D384. doi:10.1093/nar/gkv1277
  • Vlachos, I. S., K. Zagganas, M. D. Paraskevopoulou, G. Georgakilas, D. Karagkouni, T. Vergoulis, T. Dalamagas, and A. G. Hatzigeorgiou. 2015. “DIANA-miRPath v3. 0: deciphering microRNA Function with Experimental Support.” Nucleic Acids Research 43 (W1): W460–W466. doi:10.1093/nar/gkv403
  • Wang, K., J. Ruan, H. Song, J. Zhang, Y. Wo, S. Guo, and D. Cui. 2011. “Biocompatibility of Graphene Oxide.” Nanoscale Research Letters 6 (1): 8. doi:10.1007/s11671-010-9751-6
  • Wang, P., S. Huang, F. Wang, Y. Ren, M. Hehir, X. Wang, and J. Cai. 2013. “Cyclic AMP-response element regulated cell cycle arrests in cancer cells .” PLoS One 8 (6): e65661. doi:10.1371/journal.pone.0065661
  • Wernicke, S., and F. Rasche. 2006. “FANMOD: A Tool for Fast Network Motif detection.” Bioinformatics (Oxford, England) 22 (9): 1152–1153. doi:10.1093/bioinformatics/btl038
  • Wierzbicki, M., S. Jaworski, M. Kutwin, M. Grodzik, B. Strojny, N. Kurantowicz, K. Zdunek, R. Chodun, A. Chwalibog, and E. Sawosz. 2017. “Diamond, Graphite, and Graphene Oxide Nanoparticles Decrease Migration and Invasiveness in Glioblastoma Cell Lines by Impairing Extracellular Adhesion.” International Journal of Nanomedicine 12: 7241. doi:10.2147/IJN.S146193
  • Wu, Q., Y. Zhao, G. Zhao, and D. Wang. 2014. “microRNAs Control of in Vivo Toxicity from Graphene Oxide in Caenorhabditis elegans.” Nanomedicine: Nanotechnology, Biology and Medicine 10 (7): 1401–1410. doi:10.1016/j.nano.2014.04.005
  • Xiao, F., Z. Zuo, G. Cai, S. Kang, X. Gao, and T. Li. 2009. “miRecords: An Integrated Resource for microRNA–Target Interactions.” Nucleic Acids Research 37 (Database): D105–D110. doi:10.1093/nar/gkn851
  • Yang, K., Y. Li, X. Tan, R. Peng, and Z. Liu. 2013. “Behavior and Toxicity of Graphene and Its Functionalized Derivatives in Biological Systems.” Small (Weinheim an Der Bergstrasse, Germany) 9 (9–10): 1492–503. doi:10.1002/smll.201201417
  • Yang, R., M. Ren, Q. Rui, and D. Wang. 2016. “A Mir-231-Regulated Protection Mechanism against the Toxicity of Graphene Oxide in Nematode Caenorhabditis elegans.” Scientific Reports 6 (1), 32214. doi:10.1038/srep32214
  • Yin, X., L. Ju, W. Wu, Y. Xiao, S. Ying, M. Zhang, J. Lou, Z. Jia, H. Xia, and L. Zhu. 2016. “Changes of microRNAs Profiling in Mesothelial Cells Exposed to Multi-Walled Carbon Nanotubes.” Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 34: 531–534.
  • Zhang, X., Yin, J. Peng, C. Hu, W. Zhu, Z. L. I. Fan, W. C. Huang. and Q. 2011. “Distribution and Biocompatibility Studies of Graphene Oxide in Mice after Intravenous Administration.” carbon 49: 986–995. doi:10.1016/j.carbon.2010.11.005
  • Zhao, Y., R. Jia, Y. Qiao, and D. Wang. 2016. “Glycyrrhizic Acid, Active Component from Glycyrrhizae Radix, Prevents Toxicity of Graphene Oxide by Influencing Functions of microRNAs in Nematode Caenorhabditis elegans.” Nanomedicine: Nanotechnology, Biology and Medicine 12 (3): 735–744. doi:10.1016/j.nano.2015.10.008
  • Zhao, Y., Q. Wu, Y. Li, A. Nouara, R. Jia, and D. Wang. 2014. “In Vivo Translocation and Toxicity of Multi-Walled Carbon Nanotubes Are Regulated by microRNAs.” Nanoscale 6 (8): 4275–4284. doi:10.1039/c3nr06784j
  • Zhao, Y., Q. Wu, and D. Wang. 2015. “A microRNAs–mRNAs Network Involved in the Control of Graphene Oxide Toxicity in Caenorhabditis elegans.” RSC Advances 5 (112): 92394–92405. doi:10.1039/C5RA16142H
  • Zhao, Y., J. Yang, and D. Wang. 2016. “A microRNA-Mediated Insulin Signaling Pathway Regulates the Toxicity of Multi-Walled Carbon Nanotubes in Nematode Caenorhabditis elegans.” Scientific Reports 6 (1), 23234. doi:10.1038/srep23234
  • Zhao, Y., L. Zhi, Q. Wu, Y. Yu, Q. Sun, and D. Wang. 2016. “p38 MAPK-SKN-1/Nrf Signaling Cascade Is Required for Intestinal Barrier against Graphene Oxide Toxicity in Caenorhabditis elegans.” Nanotoxicology 10 (10): 1469–1479. doi:10.1080/17435390.2016.1235738
  • Zhou, T., B. Zhang, P. Wei, Y. Du, H. Zhou, M. Yu, L. Yan, et al. 2014. “Energy Metabolism Analysis Reveals the Mechanism of Inhibition of Breast Cancer Cell Metastasis by PEG-Modified Graphene Oxide Nanosheets.” Biomaterials 35 (37): 9833–9843. doi:10.1016/j.biomaterials.2014.08.033
  • Zhu, J., M. Xu, M. Gao, Z. Zhang, Y. Xu, T. Xia, and S. Liu. 2017. “Graphene Oxide Induced Perturbation to Plasma Membrane and Cytoskeletal Meshwork Sensitize Cancer Cells to Chemotherapeutic Agents.” ACS Nano 11 (3): 2637–2651. doi:10.1021/acsnano.6b07311

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.